Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005733.1 Kokia drynarioides strain JFW-HI SEQ_119971, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5863
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:1760 original size:20 final size:20

Alignment explanation


    Indices: 1719--1760  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       1709 TGAAGCATAC

                          ** *  
       1719 TTGTATCAGTAGAATTGTAG
          1 TTGTATCAGTAGAAGAGGAG

                                
       1739 TTGTATCAGTAGAAGAGGAG
          1 TTGTATCAGTAGAAGAGGAG

              
       1759 TT
          1 TT

       1761 CTACCGGTAG


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.31, C:0.05, G:0.29, T:0.36


Consensus pattern (20 bp):   
TTGTATCAGTAGAAGAGGAG

Found at i:2676 original size:16 final size:18

Alignment explanation


    Indices: 2652--2684  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       2642 ATTTGATAAA

                              
       2652 TAAATTAA-TTTCTCAAT
          1 TAAATTAATTTTCTCAAT

                             
       2669 TAAA-TAATTTTCTCAA
          1 TAAATTAATTTTCTCAA

       2685 CCCAATTATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    3  0.20
  17   12  0.80

ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45


Consensus pattern (18 bp):   
TAAATTAATTTTCTCAAT

Found at i:3988 original size:20 final size:20

Alignment explanation


    Indices: 3963--4016  Score: 72
    Period size: 20  Copynumber: 2.7  Consensus size: 20

       3953 CTCCAGTGAG

                      *  *      
       3963 ACTTCTACCGGTAGAACTCC
          1 ACTTCTACCGATACAACTCC

                     *        * 
       3983 ACTTCTACCAATACAACTTC
          1 ACTTCTACCGATACAACTCC

                          
       4003 ACTTCTACCGATAC
          1 ACTTCTACCGATAC

       4017 CTTGAAGACT


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   29  1.00

ACGTcount: A:0.30, C:0.35, G:0.07, T:0.28


Consensus pattern (20 bp):   
ACTTCTACCGATACAACTCC

Found at i:4268 original size:20 final size:21

Alignment explanation


    Indices: 4224--4270  Score: 62
    Period size: 20  Copynumber: 2.3  Consensus size: 21

       4214 AGAAATTCCT

                                 
       4224 CTTCTACTAATACAACTATAG
          1 CTTCTACTAATACAACTATAG

                    *      *     
       4245 -TTCTACTGATACAAGTAT-G
          1 CTTCTACTAATACAACTATAG

                   
       4264 CTTCTAC
          1 CTTCTAC

       4271 CGGAACAACT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  19    1  0.04
  20   22  0.96

ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36


Consensus pattern (21 bp):   
CTTCTACTAATACAACTATAG
Done.